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LitCovid-PD-FMA-UBERON

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T93","span":{"begin":350,"end":352},"obj":"Disease"},{"id":"T94","span":{"begin":506,"end":514},"obj":"Disease"},{"id":"T95","span":{"begin":579,"end":587},"obj":"Disease"},{"id":"T96","span":{"begin":707,"end":715},"obj":"Disease"},{"id":"T97","span":{"begin":778,"end":786},"obj":"Disease"},{"id":"T98","span":{"begin":820,"end":822},"obj":"Disease"}],"attributes":[{"id":"A93","pred":"mondo_id","subj":"T93","obj":"http://purl.obolibrary.org/obo/MONDO_0010725"},{"id":"A94","pred":"mondo_id","subj":"T94","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A95","pred":"mondo_id","subj":"T95","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A96","pred":"mondo_id","subj":"T96","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A97","pred":"mondo_id","subj":"T97","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A98","pred":"mondo_id","subj":"T98","obj":"http://purl.obolibrary.org/obo/MONDO_0010725"}],"text":"Finally, phosphorylation sites in N protein, a structural protein that binds to and assists with packaging viral RNA, were investigated. Most sites occurred within the N-terminal portion of the protein, at or near the RNA binding region, but avoided the C-terminal dimerization domain. The cluster of phosphorylation sites within an arginine/serine (RS)-dipeptide rich region, C-terminal to the RNA binding region (Figure 2A), is conserved in other coronavirus N proteins. This region is phosphorylated in SARS-CoV by serine-arginine (SR) protein kinases, modulating the role of SARS-CoV N protein in host translation inhibition (Peng et al., 2008). It is likely that phosphorylation of this same region in SARS-CoV-2 plays a similar role. Interestingly, in vitro inhibition of SARS-CoV N protein phosphorylation at the RS-rich region results in reduced viral load and cytopathic effects (Wu et al., 2009), highlighting its importance for viral fitness. In addition, sites spanning the sequence of the RNA binding domain, which forms a claw-like structure, have been observed (Kang et al., 2020). Several phosphorylation sites cluster in the structural model, predicted to affect the surface charge of the so-called acidic wrist region (Figure 2F) but not the positive surface charge of the RNA binding pocket. We hypothesize that this surface charge difference may modulate N protein function, potentially via allosteric regulation of RNA binding capacity."}

LitCovid-PD-CLO

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T40113","span":{"begin":45,"end":46},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T51900","span":{"begin":350,"end":352},"obj":"http://purl.obolibrary.org/obo/CLO_0008882"},{"id":"T98396","span":{"begin":422,"end":424},"obj":"http://purl.obolibrary.org/obo/CLO_0001236"},{"id":"T25732","span":{"begin":535,"end":537},"obj":"http://purl.obolibrary.org/obo/CLO_0009126"},{"id":"T69173","span":{"begin":724,"end":725},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T17099","span":{"begin":820,"end":822},"obj":"http://purl.obolibrary.org/obo/CLO_0008882"},{"id":"T46908","span":{"begin":1034,"end":1035},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"Finally, phosphorylation sites in N protein, a structural protein that binds to and assists with packaging viral RNA, were investigated. Most sites occurred within the N-terminal portion of the protein, at or near the RNA binding region, but avoided the C-terminal dimerization domain. The cluster of phosphorylation sites within an arginine/serine (RS)-dipeptide rich region, C-terminal to the RNA binding region (Figure 2A), is conserved in other coronavirus N proteins. This region is phosphorylated in SARS-CoV by serine-arginine (SR) protein kinases, modulating the role of SARS-CoV N protein in host translation inhibition (Peng et al., 2008). It is likely that phosphorylation of this same region in SARS-CoV-2 plays a similar role. Interestingly, in vitro inhibition of SARS-CoV N protein phosphorylation at the RS-rich region results in reduced viral load and cytopathic effects (Wu et al., 2009), highlighting its importance for viral fitness. In addition, sites spanning the sequence of the RNA binding domain, which forms a claw-like structure, have been observed (Kang et al., 2020). Several phosphorylation sites cluster in the structural model, predicted to affect the surface charge of the so-called acidic wrist region (Figure 2F) but not the positive surface charge of the RNA binding pocket. We hypothesize that this surface charge difference may modulate N protein function, potentially via allosteric regulation of RNA binding capacity."}

LitCovid-PD-CHEBI

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T96","span":{"begin":9,"end":24},"obj":"http://purl.obolibrary.org/obo/GO_0016310"},{"id":"T97","span":{"begin":301,"end":316},"obj":"http://purl.obolibrary.org/obo/GO_0016310"},{"id":"T98","span":{"begin":606,"end":617},"obj":"http://purl.obolibrary.org/obo/GO_0006412"},{"id":"T99","span":{"begin":668,"end":683},"obj":"http://purl.obolibrary.org/obo/GO_0016310"},{"id":"T100","span":{"begin":789,"end":812},"obj":"http://purl.obolibrary.org/obo/GO_0006468"},{"id":"T101","span":{"begin":797,"end":812},"obj":"http://purl.obolibrary.org/obo/GO_0016310"},{"id":"T102","span":{"begin":1105,"end":1120},"obj":"http://purl.obolibrary.org/obo/GO_0016310"},{"id":"T103","span":{"begin":1422,"end":1447},"obj":"http://purl.obolibrary.org/obo/GO_1905214"},{"id":"T104","span":{"begin":1422,"end":1432},"obj":"http://purl.obolibrary.org/obo/GO_0065007"}],"text":"Finally, phosphorylation sites in N protein, a structural protein that binds to and assists with packaging viral RNA, were investigated. Most sites occurred within the N-terminal portion of the protein, at or near the RNA binding region, but avoided the C-terminal dimerization domain. The cluster of phosphorylation sites within an arginine/serine (RS)-dipeptide rich region, C-terminal to the RNA binding region (Figure 2A), is conserved in other coronavirus N proteins. This region is phosphorylated in SARS-CoV by serine-arginine (SR) protein kinases, modulating the role of SARS-CoV N protein in host translation inhibition (Peng et al., 2008). It is likely that phosphorylation of this same region in SARS-CoV-2 plays a similar role. Interestingly, in vitro inhibition of SARS-CoV N protein phosphorylation at the RS-rich region results in reduced viral load and cytopathic effects (Wu et al., 2009), highlighting its importance for viral fitness. In addition, sites spanning the sequence of the RNA binding domain, which forms a claw-like structure, have been observed (Kang et al., 2020). Several phosphorylation sites cluster in the structural model, predicted to affect the surface charge of the so-called acidic wrist region (Figure 2F) but not the positive surface charge of the RNA binding pocket. We hypothesize that this surface charge difference may modulate N protein function, potentially via allosteric regulation of RNA binding capacity."}

LitCovid-PubTator

{"project":"LitCovid-PubTator","denotations":[{"id":"294","span":{"begin":168,"end":169},"obj":"Gene"},{"id":"295","span":{"begin":34,"end":35},"obj":"Gene"},{"id":"296","span":{"begin":449,"end":460},"obj":"Species"},{"id":"297","span":{"begin":506,"end":514},"obj":"Species"},{"id":"298","span":{"begin":579,"end":587},"obj":"Species"},{"id":"299","span":{"begin":707,"end":717},"obj":"Species"},{"id":"300","span":{"begin":778,"end":786},"obj":"Species"},{"id":"301","span":{"begin":333,"end":341},"obj":"Chemical"},{"id":"302","span":{"begin":342,"end":348},"obj":"Chemical"},{"id":"303","span":{"begin":354,"end":363},"obj":"Chemical"},{"id":"304","span":{"begin":518,"end":524},"obj":"Chemical"},{"id":"305","span":{"begin":939,"end":952},"obj":"Disease"}],"attributes":[{"id":"A294","pred":"tao:has_database_id","subj":"294","obj":"Gene:43740575"},{"id":"A295","pred":"tao:has_database_id","subj":"295","obj":"Gene:43740575"},{"id":"A296","pred":"tao:has_database_id","subj":"296","obj":"Tax:11118"},{"id":"A297","pred":"tao:has_database_id","subj":"297","obj":"Tax:694009"},{"id":"A298","pred":"tao:has_database_id","subj":"298","obj":"Tax:694009"},{"id":"A299","pred":"tao:has_database_id","subj":"299","obj":"Tax:2697049"},{"id":"A300","pred":"tao:has_database_id","subj":"300","obj":"Tax:694009"},{"id":"A301","pred":"tao:has_database_id","subj":"301","obj":"MESH:D001120"},{"id":"A302","pred":"tao:has_database_id","subj":"302","obj":"MESH:D012694"},{"id":"A303","pred":"tao:has_database_id","subj":"303","obj":"MESH:D004151"},{"id":"A304","pred":"tao:has_database_id","subj":"304","obj":"MESH:D012694"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}],"text":"Finally, phosphorylation sites in N protein, a structural protein that binds to and assists with packaging viral RNA, were investigated. Most sites occurred within the N-terminal portion of the protein, at or near the RNA binding region, but avoided the C-terminal dimerization domain. The cluster of phosphorylation sites within an arginine/serine (RS)-dipeptide rich region, C-terminal to the RNA binding region (Figure 2A), is conserved in other coronavirus N proteins. This region is phosphorylated in SARS-CoV by serine-arginine (SR) protein kinases, modulating the role of SARS-CoV N protein in host translation inhibition (Peng et al., 2008). It is likely that phosphorylation of this same region in SARS-CoV-2 plays a similar role. Interestingly, in vitro inhibition of SARS-CoV N protein phosphorylation at the RS-rich region results in reduced viral load and cytopathic effects (Wu et al., 2009), highlighting its importance for viral fitness. In addition, sites spanning the sequence of the RNA binding domain, which forms a claw-like structure, have been observed (Kang et al., 2020). Several phosphorylation sites cluster in the structural model, predicted to affect the surface charge of the so-called acidic wrist region (Figure 2F) but not the positive surface charge of the RNA binding pocket. We hypothesize that this surface charge difference may modulate N protein function, potentially via allosteric regulation of RNA binding capacity."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T120","span":{"begin":0,"end":136},"obj":"Sentence"},{"id":"T121","span":{"begin":137,"end":285},"obj":"Sentence"},{"id":"T122","span":{"begin":286,"end":472},"obj":"Sentence"},{"id":"T123","span":{"begin":473,"end":649},"obj":"Sentence"},{"id":"T124","span":{"begin":650,"end":739},"obj":"Sentence"},{"id":"T125","span":{"begin":740,"end":953},"obj":"Sentence"},{"id":"T126","span":{"begin":954,"end":1096},"obj":"Sentence"},{"id":"T127","span":{"begin":1097,"end":1310},"obj":"Sentence"},{"id":"T128","span":{"begin":1311,"end":1457},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Finally, phosphorylation sites in N protein, a structural protein that binds to and assists with packaging viral RNA, were investigated. Most sites occurred within the N-terminal portion of the protein, at or near the RNA binding region, but avoided the C-terminal dimerization domain. The cluster of phosphorylation sites within an arginine/serine (RS)-dipeptide rich region, C-terminal to the RNA binding region (Figure 2A), is conserved in other coronavirus N proteins. This region is phosphorylated in SARS-CoV by serine-arginine (SR) protein kinases, modulating the role of SARS-CoV N protein in host translation inhibition (Peng et al., 2008). It is likely that phosphorylation of this same region in SARS-CoV-2 plays a similar role. Interestingly, in vitro inhibition of SARS-CoV N protein phosphorylation at the RS-rich region results in reduced viral load and cytopathic effects (Wu et al., 2009), highlighting its importance for viral fitness. In addition, sites spanning the sequence of the RNA binding domain, which forms a claw-like structure, have been observed (Kang et al., 2020). Several phosphorylation sites cluster in the structural model, predicted to affect the surface charge of the so-called acidic wrist region (Figure 2F) but not the positive surface charge of the RNA binding pocket. We hypothesize that this surface charge difference may modulate N protein function, potentially via allosteric regulation of RNA binding capacity."}

2_test

{"project":"2_test","denotations":[{"id":"32645325-18631359-20773056","span":{"begin":643,"end":647},"obj":"18631359"},{"id":"32645325-19106108-20773057","span":{"begin":900,"end":904},"obj":"19106108"}],"text":"Finally, phosphorylation sites in N protein, a structural protein that binds to and assists with packaging viral RNA, were investigated. Most sites occurred within the N-terminal portion of the protein, at or near the RNA binding region, but avoided the C-terminal dimerization domain. The cluster of phosphorylation sites within an arginine/serine (RS)-dipeptide rich region, C-terminal to the RNA binding region (Figure 2A), is conserved in other coronavirus N proteins. This region is phosphorylated in SARS-CoV by serine-arginine (SR) protein kinases, modulating the role of SARS-CoV N protein in host translation inhibition (Peng et al., 2008). It is likely that phosphorylation of this same region in SARS-CoV-2 plays a similar role. Interestingly, in vitro inhibition of SARS-CoV N protein phosphorylation at the RS-rich region results in reduced viral load and cytopathic effects (Wu et al., 2009), highlighting its importance for viral fitness. In addition, sites spanning the sequence of the RNA binding domain, which forms a claw-like structure, have been observed (Kang et al., 2020). Several phosphorylation sites cluster in the structural model, predicted to affect the surface charge of the so-called acidic wrist region (Figure 2F) but not the positive surface charge of the RNA binding pocket. We hypothesize that this surface charge difference may modulate N protein function, potentially via allosteric regulation of RNA binding capacity."}

PMC:7321036 / 17903-19360 JSONTXT

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PMC:7321036 / 17903-19360 JSON TXT